BPS Virtual Event

What is This Symposium About?

Elucidating the physical landscape of biomolecules requires cross-platform efforts. From transportation mechanism of ion channels and transporters, to conformational dynamics of proteins, biophysicists have been employing multiple tools spanning different scales (e.g., cryo-EM, X-ray, NMR, fluorescent microscopy, MD simulations, molecular docking) to interrogate the molecules.

How to find good computation techniques to provide further details or predict a problem? How to select the suitable methods to corroborate the computational findings? How to reach out for collaboration and work effectively with each other? Answering these questions would help build more high-quality collaborations and promote further scientific advance in the field.

The symposium consists of four seminar-style presentations, each lasts for 20 minutes, as well as a panel discussion on how to collaborate between computational and experimental groups. The symposium mainly targets early-career scientists, such as graduate students and postdocs. It is also highly welcome for principal investigators and younger undergraduates to join us, sharing insights or questions in the panel discussion.

This event will be held on March 9, 2021 from 10:30 am - 12:30 pm in the Eastern Standard Time zone .

Symposium Program

10:30am	Understanding Potassium Channels with in Silico Electrophysiology Simulations
	Wojciech Kopec (Max Planck Institute for Biophysical Chemistry)
	Potassium channels are a class of ion channels that play critical roles in many biological functions, such as formation of the membrane potential and mediating electrical signals in excitable cells (e.g. neurons) . Structural and functional studies revealed the main features of these channels, including rapid and selective K+ ion permeation through a narrow selectivity filter (SF), channel opening and closure at the “helix bundle crossing” (activation gate), and distinct gating processes at the selectivity filter. Despite such insights, the molecular mechanisms of permeation, selectivity and gating phenomena remain largely unknown, and are further obscured by the differences between the numerous members of the potassium channel family. Nowadays, long Molecular Dynamics (MD) simulations allow studying ion channels under applied voltage, enabling a direct comparison with experimentally measured single-channel currents in electrophysiological recordings, thus coining the name ‘in silico electrophysiology’. I will present such simulations of several potassium channels, all sharing nearly identical SFs. Our simulations reveal that potassium selectivity is directly linked to the level of ion desolvation during permeation. Strict K+ selectivity is observed only upon complete desolvation that simultaneously enables high conduction rates through the channel via strong repulsion of ‘naked’ K+ ions. This addressed the long-standing and intriguing question of how potassium channels manage to permeate potassium efficiently yet selectively against slightly smaller sodium. Furthermore, we have recently confirmed the full desolvation of the K+ ions by a combination of solid-state NMR and MD simulations. Finally, our simulations revealed that the SF regulates the magnitude of ion flow through the channel, thus gating it on the molecular level. We identified an allosteric coupling that leads to subtle variations in the SF width, affecting the free energy barrier for ion permeation sufficiently to switch it from a closed to open state.

10:50am	Combining Simulation and Experiment to Study Protein Structure at Interfaces
	Sarah Alamdari (University of Washington)
	Proteins have markedly complex and diverse structures due to a high variability in size, shape, amphiphilicity, and charge needed to carry out their biological function. The interfacial behavior of adsorbed proteins govern properties such as foaming and stabilization, relevant to applications in pharmacy, biotechnology, and the food industry. Our goal is to combine experiment, simulation, and theory to understand how conformation and orientation of these complex biomolecules lead to interfacial self-assembly. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, had been unresolved. In this talk I will describe our approach to uncovering this interfacial structure by combining molecular dynamics simulation, vibrational sum frequency generation (SFG) spectroscopy, and spectral calculations to determine the conformation and orientation of lysozyme at the AWI. Computationally, two force fields are used to simulate lysozyme. With this approach we determine agreement in a single interfacial pose at high atomistic resolution. We validate the proposed structure of lysozyme by comparing signals of experimentally derived structures, to the spectra calculated from simulation, showing strong agreement by the pose predicted by MD. Lastly, we provide additional atomistic insight, discussing how pH may lead to an orientation change from head on to side-on at the interface, explaining previous discrepancies in the literature with regards to the thickness of the experimentally derived monolayers. This work provides a template for future studies of proteins at interfaces to make maximum use of integrated computational and experimental approaches.

11:10am	Activation and Desensitization of Glycine Receptor in Lipid Nanodiscs: Insights from Structures and Simulations
	Arvind Kumar (Case Western Reserve University)
	Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.

11:30am	Mechanisms of Gating and Lipid Transport by TMEM16 Scramblases Revealed by Synergistic Experimental and Computational studies
	Maria Falzone (Rockefeller University)
	When activated, plasma membrane scramblases transport lipids rapidly down their concentration gradients, collapsing the asymmetry of eukaryotic cell membranes and initiating various signaling cascades of physiological importance such as blood coagulation and apoptosis. The TMEM16 family of membrane proteins is comprised of Ca2+-dependent chloride channels and dual function scramblase/non-selective ion channels. The TMEM16s are dimeric proteins, where each monomer forms an independent translocation pathway for ions and lipids that is gated by Ca2+ and other factors. To understand the gating of this pathway and the translocation mechanism of ions and phospholipids through it, we used collaborative computational and experimental approaches. Molecular dynamics simulations on the fungal nhTMEM16 identified a hydrophobic lock that regulates the transition between the lipid scramblase and channel conformations of the pathway. Concurrent biochemical and structural studies supported the role of the hydrophobic lock in this process and identified the ion conductive conformation of the scramblase. Structural studies revealed that TMEM16 scramblases bend and remodel the surrounding membrane. We proposed that this remodeling enabled the lipid translocation process. Indeed, novel high-resolution structures of the fungal afTMEM16 scramblase in a scrambling-competent conformation revealed several associated lipids that adopt dramatically distorted poses as they approach and enter the opened translocation pathway. Computational studies aiming to understand the mechanistic significance of these observations show a very similar pattern of lipids with long dwell times. The long MD trajectories allowed for the quantification of the residence time at the sites, supporting the importance of these lipid interaction sites. Together, these results provide a direct visualization of the rearrangements induced by an activated scramblase on the surrounding membrane to enable lipid transport. These examples highlight the powerful mechanistic insights that can be obtained only through the synergistic use of experimental and computational studies.

11:50am	Panel Discussion
	Panelists: Wojciech Kopec, Sarah Alamdari, Arvind Kumar, Maria Falzone
	In this section discussions on how to smoothly and effectively collaborate between experimental and computational groups will be carried out. Panelists will share their tips and advice on such collaboration. Meeting attendees are encouraged to ask questions they have on this topic as well as sharing their experiences.

Organizers

The symposium is hosted by Shasha Feng (Lehigh University) and Shashank Pant (University of Illinois at Urbana-Champaign). For more information contact shf317@lehigh.edu, pant5@illinois.edu.